Starting phenix.real_space_refine on Mon Nov 17 22:06:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dmb_7963/11_2025/6dmb_7963.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dmb_7963/11_2025/6dmb_7963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6dmb_7963/11_2025/6dmb_7963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dmb_7963/11_2025/6dmb_7963.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dmb_7963/11_2025/6dmb_7963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dmb_7963/11_2025/6dmb_7963.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 768 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 5189 2.51 5 N 1290 2.21 5 O 1424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7945 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7777 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 946} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 4, 'PHE:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Unusual residues: {'NAG': 5, 'Y01': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.80, per 1000 atoms: 0.23 Number of scatterers: 7945 At special positions: 0 Unit cell: (94.917, 77.461, 141.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1424 8.00 N 1290 7.00 C 5189 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 327 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 304 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1801 " - " ASN A 312 " " NAG A1802 " - " ASN A 349 " " NAG A1803 " - " ASN A 414 " " NAG A1804 " - " ASN A 875 " " NAG A1807 " - " ASN A 141 " " NAG B 1 " - " ASN A1000 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 296.1 milliseconds 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1856 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 5 sheets defined 60.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 74 through 96 removed outlier: 4.175A pdb=" N TRP A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.807A pdb=" N PHE A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 102 " --> pdb=" O CYS A 98 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.649A pdb=" N TRP A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 171 through 185 Processing helix chain 'A' and resid 216 through 222 Processing helix chain 'A' and resid 230 through 234 removed outlier: 3.685A pdb=" N ASP A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 234' Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.534A pdb=" N ASN A 258 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 259 " --> pdb=" O TRP A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 259' Processing helix chain 'A' and resid 260 through 271 removed outlier: 4.069A pdb=" N ILE A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 285 removed outlier: 3.751A pdb=" N ALA A 285 " --> pdb=" O MET A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.790A pdb=" N ILE A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 388 through 411 removed outlier: 3.657A pdb=" N GLU A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 439 through 457 removed outlier: 3.661A pdb=" N LEU A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N MET A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 491 removed outlier: 3.842A pdb=" N LEU A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 506 through 526 removed outlier: 3.688A pdb=" N VAL A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 564 removed outlier: 3.890A pdb=" N THR A 544 " --> pdb=" O CYS A 540 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ALA A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N SER A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 605 removed outlier: 4.022A pdb=" N GLN A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Proline residue: A 593 - end of helix removed outlier: 4.147A pdb=" N SER A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASP A 605 " --> pdb=" O TYR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 removed outlier: 3.713A pdb=" N LYS A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 745 removed outlier: 3.619A pdb=" N LEU A 745 " --> pdb=" O PRO A 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 742 through 745' Processing helix chain 'A' and resid 746 through 749 Processing helix chain 'A' and resid 750 through 770 removed outlier: 4.205A pdb=" N ILE A 754 " --> pdb=" O LYS A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 798 Processing helix chain 'A' and resid 815 through 828 removed outlier: 3.654A pdb=" N TYR A 820 " --> pdb=" O GLN A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 863 removed outlier: 3.688A pdb=" N TYR A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 888 removed outlier: 3.707A pdb=" N VAL A 881 " --> pdb=" O SER A 877 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 882 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 883 " --> pdb=" O ASP A 879 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 888 " --> pdb=" O TYR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 903 Processing helix chain 'A' and resid 919 through 930 removed outlier: 3.565A pdb=" N LEU A 923 " --> pdb=" O PHE A 919 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 924 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA A 925 " --> pdb=" O ILE A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 937 removed outlier: 3.861A pdb=" N SER A 937 " --> pdb=" O ALA A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1004 removed outlier: 3.760A pdb=" N ILE A 997 " --> pdb=" O LYS A 993 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A1003 " --> pdb=" O SER A 999 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A1004 " --> pdb=" O ASN A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1018 Processing helix chain 'A' and resid 1019 through 1022 Processing helix chain 'A' and resid 1026 through 1046 removed outlier: 3.510A pdb=" N PHE A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1075 removed outlier: 3.796A pdb=" N GLY A1075 " --> pdb=" O MET A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1106 removed outlier: 3.556A pdb=" N VAL A1084 " --> pdb=" O ALA A1080 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A1085 " --> pdb=" O VAL A1081 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE A1096 " --> pdb=" O ILE A1092 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1122 removed outlier: 3.525A pdb=" N ALA A1118 " --> pdb=" O ARG A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1138 Processing helix chain 'A' and resid 1146 through 1155 Processing helix chain 'A' and resid 1155 through 1178 Proline residue: A1172 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 363 Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 331 removed outlier: 4.751A pdb=" N SER A 331 " --> pdb=" O MET A 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 348 removed outlier: 7.242A pdb=" N VAL A 347 " --> pdb=" O VAL A 355 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 975 through 978 removed outlier: 3.738A pdb=" N TYR A 804 " --> pdb=" O ASN A1011 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2419 1.34 - 1.46: 1964 1.46 - 1.59: 3690 1.59 - 1.71: 0 1.71 - 1.83: 69 Bond restraints: 8142 Sorted by residual: bond pdb=" CAY Y01 A1809 " pdb=" OAW Y01 A1809 " ideal model delta sigma weight residual 1.332 1.462 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" CAY Y01 A1808 " pdb=" OAW Y01 A1808 " ideal model delta sigma weight residual 1.332 1.452 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C ASP A 293 " pdb=" N ARG A 294 " ideal model delta sigma weight residual 1.331 1.252 0.079 1.59e-02 3.96e+03 2.47e+01 bond pdb=" CAX Y01 A1808 " pdb=" OAH Y01 A1808 " ideal model delta sigma weight residual 1.248 1.328 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" CAX Y01 A1809 " pdb=" OAH Y01 A1809 " ideal model delta sigma weight residual 1.248 1.328 -0.080 2.00e-02 2.50e+03 1.60e+01 ... (remaining 8137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 10629 3.01 - 6.01: 359 6.01 - 9.02: 83 9.02 - 12.02: 10 12.02 - 15.03: 4 Bond angle restraints: 11085 Sorted by residual: angle pdb=" C LEU A 458 " pdb=" N ARG A 459 " pdb=" CA ARG A 459 " ideal model delta sigma weight residual 121.54 132.51 -10.97 1.91e+00 2.74e-01 3.30e+01 angle pdb=" N VAL A 908 " pdb=" CA VAL A 908 " pdb=" C VAL A 908 " ideal model delta sigma weight residual 113.53 108.53 5.00 9.80e-01 1.04e+00 2.60e+01 angle pdb=" C GLU A 836 " pdb=" N ASN A 837 " pdb=" CA ASN A 837 " ideal model delta sigma weight residual 121.54 130.85 -9.31 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C LEU A1048 " pdb=" N ASN A1049 " pdb=" CA ASN A1049 " ideal model delta sigma weight residual 121.80 133.18 -11.38 2.44e+00 1.68e-01 2.18e+01 angle pdb=" N GLU A 947 " pdb=" CA GLU A 947 " pdb=" C GLU A 947 " ideal model delta sigma weight residual 110.91 116.30 -5.39 1.17e+00 7.31e-01 2.12e+01 ... (remaining 11080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.57: 4738 24.57 - 49.14: 227 49.14 - 73.71: 23 73.71 - 98.28: 6 98.28 - 122.85: 3 Dihedral angle restraints: 4997 sinusoidal: 2111 harmonic: 2886 Sorted by residual: dihedral pdb=" CA ASN A1049 " pdb=" C ASN A1049 " pdb=" N PRO A1050 " pdb=" CA PRO A1050 " ideal model delta harmonic sigma weight residual 180.00 -120.68 -59.32 0 5.00e+00 4.00e-02 1.41e+02 dihedral pdb=" CA LYS A 867 " pdb=" C LYS A 867 " pdb=" N ILE A 868 " pdb=" CA ILE A 868 " ideal model delta harmonic sigma weight residual -180.00 -132.90 -47.10 0 5.00e+00 4.00e-02 8.87e+01 dihedral pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " pdb=" SG CYS A 304 " pdb=" CB CYS A 304 " ideal model delta sinusoidal sigma weight residual 93.00 166.11 -73.11 1 1.00e+01 1.00e-02 6.81e+01 ... (remaining 4994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1079 0.091 - 0.182: 193 0.182 - 0.273: 14 0.273 - 0.363: 2 0.363 - 0.454: 1 Chirality restraints: 1289 Sorted by residual: chirality pdb=" C1 NAG A1804 " pdb=" ND2 ASN A 875 " pdb=" C2 NAG A1804 " pdb=" O5 NAG A1804 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CB ILE A 531 " pdb=" CA ILE A 531 " pdb=" CG1 ILE A 531 " pdb=" CG2 ILE A 531 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C1 NAG A1801 " pdb=" ND2 ASN A 312 " pdb=" C2 NAG A1801 " pdb=" O5 NAG A1801 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1286 not shown) Planarity restraints: 1380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 869 " -0.063 5.00e-02 4.00e+02 9.52e-02 1.45e+01 pdb=" N PRO A 870 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 870 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 870 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 812 " 0.051 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO A 813 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 813 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 813 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A1081 " 0.051 5.00e-02 4.00e+02 7.58e-02 9.20e+00 pdb=" N PRO A1082 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A1082 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A1082 " 0.043 5.00e-02 4.00e+02 ... (remaining 1377 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1940 2.79 - 3.32: 7486 3.32 - 3.85: 12883 3.85 - 4.37: 13993 4.37 - 4.90: 23612 Nonbonded interactions: 59914 Sorted by model distance: nonbonded pdb=" O MET A 956 " pdb=" OG1 THR A 959 " model vdw 2.266 3.040 nonbonded pdb=" O GLY A 774 " pdb=" OH TYR A1021 " model vdw 2.275 3.040 nonbonded pdb=" O CYS A 998 " pdb=" OG1 THR A1002 " model vdw 2.295 3.040 nonbonded pdb=" O TYR A 452 " pdb=" OG1 THR A 456 " model vdw 2.317 3.040 nonbonded pdb=" O ASN A 120 " pdb=" OG SER A 494 " model vdw 2.338 3.040 ... (remaining 59909 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.600 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.130 8152 Z= 0.398 Angle : 1.388 15.377 11112 Z= 0.695 Chirality : 0.068 0.454 1289 Planarity : 0.009 0.095 1374 Dihedral : 13.898 122.852 3132 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.61 % Allowed : 13.18 % Favored : 86.21 % Rotamer: Outliers : 1.94 % Allowed : 8.74 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 4.65 % Twisted General : 0.63 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.21), residues: 986 helix: -2.31 (0.17), residues: 525 sheet: -3.36 (0.56), residues: 52 loop : -3.90 (0.26), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 255 TYR 0.032 0.003 TYR A 222 PHE 0.045 0.004 PHE A1015 TRP 0.034 0.004 TRP A 337 HIS 0.011 0.002 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00887 ( 8142) covalent geometry : angle 1.36228 (11085) SS BOND : bond 0.00589 ( 3) SS BOND : angle 1.75782 ( 6) hydrogen bonds : bond 0.15256 ( 389) hydrogen bonds : angle 6.79275 ( 1134) link_BETA1-4 : bond 0.00204 ( 1) link_BETA1-4 : angle 1.04453 ( 3) link_NAG-ASN : bond 0.01317 ( 6) link_NAG-ASN : angle 6.67683 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 TRP cc_start: 0.7803 (m100) cc_final: 0.7106 (m-10) REVERT: A 183 LEU cc_start: 0.9037 (tp) cc_final: 0.8744 (tt) REVERT: A 374 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7876 (mm-30) REVERT: A 416 THR cc_start: 0.8533 (p) cc_final: 0.8251 (t) REVERT: A 455 LEU cc_start: 0.8678 (mm) cc_final: 0.8428 (tt) REVERT: A 490 LEU cc_start: 0.8894 (mm) cc_final: 0.8400 (tt) REVERT: A 550 LEU cc_start: 0.9214 (tp) cc_final: 0.8872 (tp) REVERT: A 598 MET cc_start: 0.8044 (mmm) cc_final: 0.7783 (tmm) REVERT: A 988 VAL cc_start: 0.9322 (t) cc_final: 0.8273 (m) REVERT: A 1029 LEU cc_start: 0.8798 (tt) cc_final: 0.8477 (mm) REVERT: A 1076 ILE cc_start: 0.9051 (mm) cc_final: 0.8837 (mm) REVERT: A 1128 ASP cc_start: 0.7284 (m-30) cc_final: 0.6992 (m-30) REVERT: A 1146 ASP cc_start: 0.7669 (t0) cc_final: 0.7248 (t0) REVERT: A 1165 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8648 (mt) outliers start: 16 outliers final: 4 residues processed: 226 average time/residue: 0.0813 time to fit residues: 25.1433 Evaluate side-chains 116 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1165 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 95 GLN ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN A 375 HIS A 409 GLN A 496 ASN A 584 ASN A 802 ASN A 828 ASN A 846 HIS A 856 GLN A 872 ASN A 929 ASN A1099 HIS A1112 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.110375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.093965 restraints weight = 19583.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.096390 restraints weight = 11342.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.098078 restraints weight = 7855.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.099123 restraints weight = 6070.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.099983 restraints weight = 5117.271| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8152 Z= 0.154 Angle : 0.875 11.314 11112 Z= 0.419 Chirality : 0.044 0.254 1289 Planarity : 0.006 0.071 1374 Dihedral : 9.250 59.127 1368 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.46 % Favored : 88.24 % Rotamer: Outliers : 5.34 % Allowed : 15.53 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.25), residues: 986 helix: -0.78 (0.20), residues: 569 sheet: -2.70 (0.68), residues: 46 loop : -3.73 (0.28), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 962 TYR 0.021 0.001 TYR A 740 PHE 0.030 0.002 PHE A 800 TRP 0.016 0.002 TRP A 236 HIS 0.006 0.001 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8142) covalent geometry : angle 0.85261 (11085) SS BOND : bond 0.00263 ( 3) SS BOND : angle 0.82964 ( 6) hydrogen bonds : bond 0.05244 ( 389) hydrogen bonds : angle 5.03053 ( 1134) link_BETA1-4 : bond 0.00168 ( 1) link_BETA1-4 : angle 0.72350 ( 3) link_NAG-ASN : bond 0.00944 ( 6) link_NAG-ASN : angle 4.95376 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 TRP cc_start: 0.7607 (m100) cc_final: 0.7029 (m-10) REVERT: A 183 LEU cc_start: 0.8960 (tp) cc_final: 0.8644 (tt) REVERT: A 416 THR cc_start: 0.8340 (p) cc_final: 0.8126 (t) REVERT: A 432 LYS cc_start: 0.8997 (tmtt) cc_final: 0.8583 (tmtt) REVERT: A 455 LEU cc_start: 0.8258 (mm) cc_final: 0.8046 (tt) REVERT: A 490 LEU cc_start: 0.8557 (mm) cc_final: 0.8135 (tt) outliers start: 44 outliers final: 20 residues processed: 173 average time/residue: 0.0719 time to fit residues: 17.9279 Evaluate side-chains 120 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 856 GLN Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 950 HIS Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 34 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 289 HIS A 576 GLN A 584 ASN A 853 GLN A 856 GLN A 889 GLN ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.108505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.092305 restraints weight = 19636.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.094694 restraints weight = 11295.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.096356 restraints weight = 7786.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.097391 restraints weight = 5980.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.098232 restraints weight = 5013.479| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8152 Z= 0.163 Angle : 0.846 11.151 11112 Z= 0.403 Chirality : 0.045 0.298 1289 Planarity : 0.006 0.072 1374 Dihedral : 8.380 71.991 1364 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.17 % Favored : 87.63 % Rotamer: Outliers : 5.95 % Allowed : 17.23 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.26), residues: 986 helix: -0.10 (0.21), residues: 576 sheet: -2.06 (0.76), residues: 51 loop : -3.62 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1113 TYR 0.021 0.002 TYR A 740 PHE 0.025 0.002 PHE A1104 TRP 0.018 0.002 TRP A 78 HIS 0.007 0.001 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8142) covalent geometry : angle 0.82681 (11085) SS BOND : bond 0.00238 ( 3) SS BOND : angle 0.77343 ( 6) hydrogen bonds : bond 0.04881 ( 389) hydrogen bonds : angle 4.70827 ( 1134) link_BETA1-4 : bond 0.00195 ( 1) link_BETA1-4 : angle 0.70573 ( 3) link_NAG-ASN : bond 0.00814 ( 6) link_NAG-ASN : angle 4.49824 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 118 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8817 (tp) cc_final: 0.8523 (tt) REVERT: A 192 MET cc_start: 0.4526 (pmm) cc_final: 0.3947 (pmm) REVERT: A 198 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.6961 (mtmp) REVERT: A 360 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8752 (pp) REVERT: A 416 THR cc_start: 0.8433 (p) cc_final: 0.8132 (t) REVERT: A 455 LEU cc_start: 0.8400 (mm) cc_final: 0.8171 (tt) REVERT: A 490 LEU cc_start: 0.8592 (mm) cc_final: 0.8162 (tt) outliers start: 49 outliers final: 26 residues processed: 155 average time/residue: 0.0678 time to fit residues: 15.5979 Evaluate side-chains 132 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 950 HIS Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1149 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 51 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.108062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.091851 restraints weight = 19982.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.094256 restraints weight = 11649.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.095880 restraints weight = 8032.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.096898 restraints weight = 6207.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.097598 restraints weight = 5234.538| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8152 Z= 0.167 Angle : 0.832 10.602 11112 Z= 0.394 Chirality : 0.045 0.309 1289 Planarity : 0.005 0.075 1374 Dihedral : 8.065 59.307 1364 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer: Outliers : 5.34 % Allowed : 20.15 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.27), residues: 986 helix: 0.18 (0.22), residues: 577 sheet: -1.94 (0.76), residues: 51 loop : -3.62 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 255 TYR 0.022 0.001 TYR A 740 PHE 0.019 0.002 PHE A 800 TRP 0.015 0.002 TRP A 78 HIS 0.006 0.001 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 8142) covalent geometry : angle 0.81773 (11085) SS BOND : bond 0.00228 ( 3) SS BOND : angle 0.73656 ( 6) hydrogen bonds : bond 0.04744 ( 389) hydrogen bonds : angle 4.64164 ( 1134) link_BETA1-4 : bond 0.00164 ( 1) link_BETA1-4 : angle 0.55937 ( 3) link_NAG-ASN : bond 0.00510 ( 6) link_NAG-ASN : angle 3.94356 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 112 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.4173 (pmm) cc_final: 0.3610 (pmm) REVERT: A 360 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8748 (pp) REVERT: A 416 THR cc_start: 0.8407 (p) cc_final: 0.8114 (t) REVERT: A 455 LEU cc_start: 0.8385 (mm) cc_final: 0.8147 (tt) REVERT: A 490 LEU cc_start: 0.8550 (mm) cc_final: 0.8102 (tt) outliers start: 44 outliers final: 31 residues processed: 146 average time/residue: 0.0614 time to fit residues: 13.5358 Evaluate side-chains 134 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1160 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 84 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.110372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.093720 restraints weight = 19929.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.096205 restraints weight = 11654.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.097883 restraints weight = 8070.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.099039 restraints weight = 6261.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.099443 restraints weight = 5250.383| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8152 Z= 0.142 Angle : 0.806 10.919 11112 Z= 0.376 Chirality : 0.043 0.255 1289 Planarity : 0.005 0.078 1374 Dihedral : 7.705 58.392 1362 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.27 % Favored : 87.73 % Rotamer: Outliers : 5.34 % Allowed : 21.36 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.28), residues: 986 helix: 0.41 (0.22), residues: 577 sheet: -1.79 (0.77), residues: 51 loop : -3.44 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.023 0.001 TYR A 740 PHE 0.022 0.002 PHE A1153 TRP 0.017 0.002 TRP A 256 HIS 0.005 0.001 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8142) covalent geometry : angle 0.79357 (11085) SS BOND : bond 0.00148 ( 3) SS BOND : angle 0.61591 ( 6) hydrogen bonds : bond 0.04398 ( 389) hydrogen bonds : angle 4.47862 ( 1134) link_BETA1-4 : bond 0.00195 ( 1) link_BETA1-4 : angle 0.66438 ( 3) link_NAG-ASN : bond 0.00547 ( 6) link_NAG-ASN : angle 3.54797 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 117 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8246 (m-40) cc_final: 0.7566 (p0) REVERT: A 183 LEU cc_start: 0.8666 (tp) cc_final: 0.8377 (tt) REVERT: A 192 MET cc_start: 0.3866 (pmm) cc_final: 0.3193 (pmm) REVERT: A 198 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6952 (mtmp) REVERT: A 360 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8742 (pp) REVERT: A 416 THR cc_start: 0.8359 (p) cc_final: 0.8002 (t) REVERT: A 490 LEU cc_start: 0.8507 (mm) cc_final: 0.8045 (tt) REVERT: A 493 ILE cc_start: 0.6481 (OUTLIER) cc_final: 0.6172 (mm) REVERT: A 905 GLN cc_start: 0.6805 (tp-100) cc_final: 0.6563 (tp40) REVERT: A 986 ASP cc_start: 0.8070 (m-30) cc_final: 0.7851 (t0) REVERT: A 1048 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7360 (tt) REVERT: A 1076 ILE cc_start: 0.9051 (mm) cc_final: 0.8836 (mm) outliers start: 44 outliers final: 30 residues processed: 147 average time/residue: 0.0675 time to fit residues: 14.9535 Evaluate side-chains 139 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 27 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 52 optimal weight: 0.2980 chunk 4 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.108982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.092316 restraints weight = 19887.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.094738 restraints weight = 11522.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.096425 restraints weight = 7933.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.097611 restraints weight = 6132.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.098336 restraints weight = 5098.057| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 8152 Z= 0.211 Angle : 1.198 59.193 11112 Z= 0.599 Chirality : 0.050 0.781 1289 Planarity : 0.005 0.079 1374 Dihedral : 7.863 58.390 1362 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % Rotamer: Outliers : 5.10 % Allowed : 22.21 % Favored : 72.69 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.28), residues: 986 helix: 0.45 (0.22), residues: 576 sheet: -1.81 (0.77), residues: 51 loop : -3.45 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1113 TYR 0.020 0.001 TYR A 740 PHE 0.018 0.002 PHE A1153 TRP 0.013 0.002 TRP A 78 HIS 0.004 0.001 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 8142) covalent geometry : angle 1.13583 (11085) SS BOND : bond 0.00223 ( 3) SS BOND : angle 0.64731 ( 6) hydrogen bonds : bond 0.04489 ( 389) hydrogen bonds : angle 4.49680 ( 1134) link_BETA1-4 : bond 0.00049 ( 1) link_BETA1-4 : angle 0.66113 ( 3) link_NAG-ASN : bond 0.00717 ( 6) link_NAG-ASN : angle 9.57714 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 106 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8263 (m-40) cc_final: 0.7535 (p0) REVERT: A 183 LEU cc_start: 0.8681 (tp) cc_final: 0.8397 (tt) REVERT: A 192 MET cc_start: 0.3914 (pmm) cc_final: 0.3247 (pmm) REVERT: A 198 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7001 (mtmp) REVERT: A 360 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8745 (pp) REVERT: A 416 THR cc_start: 0.8383 (p) cc_final: 0.8016 (t) REVERT: A 490 LEU cc_start: 0.8572 (mm) cc_final: 0.8117 (tt) REVERT: A 493 ILE cc_start: 0.6537 (OUTLIER) cc_final: 0.6166 (mm) REVERT: A 1048 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7370 (tt) REVERT: A 1076 ILE cc_start: 0.9108 (mm) cc_final: 0.8845 (mm) outliers start: 42 outliers final: 34 residues processed: 137 average time/residue: 0.0702 time to fit residues: 14.6263 Evaluate side-chains 138 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 1 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 0.0470 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.109349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.092492 restraints weight = 20046.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.095026 restraints weight = 11570.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.096761 restraints weight = 7968.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.097902 restraints weight = 6162.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.098620 restraints weight = 5167.528| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 8152 Z= 0.211 Angle : 1.198 59.193 11112 Z= 0.599 Chirality : 0.050 0.781 1289 Planarity : 0.005 0.079 1374 Dihedral : 7.863 58.390 1362 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % Rotamer: Outliers : 4.61 % Allowed : 23.06 % Favored : 72.33 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.28), residues: 986 helix: 0.45 (0.22), residues: 576 sheet: -1.81 (0.77), residues: 51 loop : -3.45 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1113 TYR 0.020 0.001 TYR A 740 PHE 0.018 0.002 PHE A1153 TRP 0.013 0.002 TRP A 78 HIS 0.004 0.001 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 8142) covalent geometry : angle 1.13583 (11085) SS BOND : bond 0.00223 ( 3) SS BOND : angle 0.64731 ( 6) hydrogen bonds : bond 0.04489 ( 389) hydrogen bonds : angle 4.49680 ( 1134) link_BETA1-4 : bond 0.00049 ( 1) link_BETA1-4 : angle 0.66113 ( 3) link_NAG-ASN : bond 0.00717 ( 6) link_NAG-ASN : angle 9.57714 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8264 (m-40) cc_final: 0.7540 (p0) REVERT: A 192 MET cc_start: 0.3861 (pmm) cc_final: 0.3204 (pmm) REVERT: A 198 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6977 (mtmp) REVERT: A 360 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8750 (pp) REVERT: A 416 THR cc_start: 0.8384 (p) cc_final: 0.8014 (t) REVERT: A 490 LEU cc_start: 0.8572 (mm) cc_final: 0.8115 (tt) REVERT: A 493 ILE cc_start: 0.6544 (OUTLIER) cc_final: 0.6177 (mm) REVERT: A 1048 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7364 (tt) REVERT: A 1076 ILE cc_start: 0.9106 (mm) cc_final: 0.8842 (mm) outliers start: 38 outliers final: 34 residues processed: 128 average time/residue: 0.0656 time to fit residues: 12.8493 Evaluate side-chains 138 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 5 optimal weight: 0.0470 chunk 27 optimal weight: 40.0000 chunk 40 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.108650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.091957 restraints weight = 20094.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.094442 restraints weight = 11563.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.096171 restraints weight = 7948.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097343 restraints weight = 6133.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.098092 restraints weight = 5099.702| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 8152 Z= 0.211 Angle : 1.198 59.193 11112 Z= 0.599 Chirality : 0.050 0.781 1289 Planarity : 0.005 0.079 1374 Dihedral : 7.863 58.390 1362 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % Rotamer: Outliers : 4.61 % Allowed : 23.18 % Favored : 72.21 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.28), residues: 986 helix: 0.45 (0.22), residues: 576 sheet: -1.81 (0.77), residues: 51 loop : -3.45 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1113 TYR 0.020 0.001 TYR A 740 PHE 0.018 0.002 PHE A1153 TRP 0.013 0.002 TRP A 78 HIS 0.004 0.001 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 8142) covalent geometry : angle 1.13583 (11085) SS BOND : bond 0.00223 ( 3) SS BOND : angle 0.64731 ( 6) hydrogen bonds : bond 0.04489 ( 389) hydrogen bonds : angle 4.49680 ( 1134) link_BETA1-4 : bond 0.00049 ( 1) link_BETA1-4 : angle 0.66113 ( 3) link_NAG-ASN : bond 0.00717 ( 6) link_NAG-ASN : angle 9.57714 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8259 (m-40) cc_final: 0.7550 (p0) REVERT: A 192 MET cc_start: 0.3806 (pmm) cc_final: 0.3165 (pmm) REVERT: A 198 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6950 (mtmp) REVERT: A 360 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8761 (pp) REVERT: A 416 THR cc_start: 0.8372 (p) cc_final: 0.8006 (t) REVERT: A 490 LEU cc_start: 0.8559 (mm) cc_final: 0.8106 (tt) REVERT: A 493 ILE cc_start: 0.6550 (OUTLIER) cc_final: 0.6180 (mm) REVERT: A 1048 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7374 (tt) REVERT: A 1076 ILE cc_start: 0.9096 (mm) cc_final: 0.8836 (mm) outliers start: 38 outliers final: 34 residues processed: 128 average time/residue: 0.0653 time to fit residues: 12.7770 Evaluate side-chains 138 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 35 optimal weight: 0.0870 chunk 9 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.109311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.092469 restraints weight = 19979.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.094969 restraints weight = 11565.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.096667 restraints weight = 7997.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.097829 restraints weight = 6204.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.098574 restraints weight = 5194.690| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 8152 Z= 0.211 Angle : 1.198 59.193 11112 Z= 0.599 Chirality : 0.050 0.781 1289 Planarity : 0.005 0.079 1374 Dihedral : 7.863 58.390 1362 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % Rotamer: Outliers : 4.61 % Allowed : 23.18 % Favored : 72.21 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.28), residues: 986 helix: 0.45 (0.22), residues: 576 sheet: -1.81 (0.77), residues: 51 loop : -3.45 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1113 TYR 0.020 0.001 TYR A 740 PHE 0.018 0.002 PHE A1153 TRP 0.013 0.002 TRP A 78 HIS 0.004 0.001 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 8142) covalent geometry : angle 1.13583 (11085) SS BOND : bond 0.00223 ( 3) SS BOND : angle 0.64731 ( 6) hydrogen bonds : bond 0.04489 ( 389) hydrogen bonds : angle 4.49680 ( 1134) link_BETA1-4 : bond 0.00049 ( 1) link_BETA1-4 : angle 0.66113 ( 3) link_NAG-ASN : bond 0.00717 ( 6) link_NAG-ASN : angle 9.57714 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8263 (m-40) cc_final: 0.7543 (p0) REVERT: A 192 MET cc_start: 0.3854 (pmm) cc_final: 0.3198 (pmm) REVERT: A 198 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6978 (mtmp) REVERT: A 360 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8749 (pp) REVERT: A 416 THR cc_start: 0.8386 (p) cc_final: 0.8016 (t) REVERT: A 490 LEU cc_start: 0.8573 (mm) cc_final: 0.8113 (tt) REVERT: A 493 ILE cc_start: 0.6549 (OUTLIER) cc_final: 0.6179 (mm) REVERT: A 1048 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7365 (tt) REVERT: A 1076 ILE cc_start: 0.9105 (mm) cc_final: 0.8843 (mm) outliers start: 38 outliers final: 34 residues processed: 128 average time/residue: 0.0653 time to fit residues: 12.7592 Evaluate side-chains 138 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.109314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.092457 restraints weight = 20057.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.094954 restraints weight = 11594.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.096645 restraints weight = 8015.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.097816 restraints weight = 6223.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.098565 restraints weight = 5205.295| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 8152 Z= 0.210 Angle : 1.198 59.110 11112 Z= 0.599 Chirality : 0.050 0.780 1289 Planarity : 0.005 0.079 1374 Dihedral : 7.863 58.391 1362 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % Rotamer: Outliers : 4.61 % Allowed : 23.18 % Favored : 72.21 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.28), residues: 986 helix: 0.45 (0.22), residues: 576 sheet: -1.81 (0.77), residues: 51 loop : -3.45 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1113 TYR 0.020 0.001 TYR A 740 PHE 0.018 0.002 PHE A1153 TRP 0.013 0.002 TRP A 78 HIS 0.004 0.001 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 8142) covalent geometry : angle 1.13520 (11085) SS BOND : bond 0.00221 ( 3) SS BOND : angle 0.64739 ( 6) hydrogen bonds : bond 0.04488 ( 389) hydrogen bonds : angle 4.49684 ( 1134) link_BETA1-4 : bond 0.00061 ( 1) link_BETA1-4 : angle 0.66787 ( 3) link_NAG-ASN : bond 0.00714 ( 6) link_NAG-ASN : angle 9.58977 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8258 (m-40) cc_final: 0.7555 (p0) REVERT: A 192 MET cc_start: 0.3812 (pmm) cc_final: 0.3169 (pmm) REVERT: A 198 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6958 (mtmp) REVERT: A 360 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8762 (pp) REVERT: A 416 THR cc_start: 0.8376 (p) cc_final: 0.8009 (t) REVERT: A 490 LEU cc_start: 0.8560 (mm) cc_final: 0.8106 (tt) REVERT: A 493 ILE cc_start: 0.6554 (OUTLIER) cc_final: 0.6184 (mm) REVERT: A 1048 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7370 (tt) REVERT: A 1076 ILE cc_start: 0.9097 (mm) cc_final: 0.8838 (mm) outliers start: 38 outliers final: 34 residues processed: 128 average time/residue: 0.0654 time to fit residues: 12.8125 Evaluate side-chains 138 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 21 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.109314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.092471 restraints weight = 19958.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.094977 restraints weight = 11567.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.096696 restraints weight = 7980.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.097859 restraints weight = 6184.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.098678 restraints weight = 5169.462| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 8152 Z= 0.210 Angle : 1.198 59.110 11112 Z= 0.599 Chirality : 0.050 0.780 1289 Planarity : 0.005 0.079 1374 Dihedral : 7.863 58.391 1362 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % Rotamer: Outliers : 4.61 % Allowed : 23.18 % Favored : 72.21 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.28), residues: 986 helix: 0.45 (0.22), residues: 576 sheet: -1.81 (0.77), residues: 51 loop : -3.45 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1113 TYR 0.020 0.001 TYR A 740 PHE 0.018 0.002 PHE A1153 TRP 0.013 0.002 TRP A 78 HIS 0.004 0.001 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 8142) covalent geometry : angle 1.13520 (11085) SS BOND : bond 0.00221 ( 3) SS BOND : angle 0.64739 ( 6) hydrogen bonds : bond 0.04488 ( 389) hydrogen bonds : angle 4.49684 ( 1134) link_BETA1-4 : bond 0.00061 ( 1) link_BETA1-4 : angle 0.66789 ( 3) link_NAG-ASN : bond 0.00714 ( 6) link_NAG-ASN : angle 9.58985 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1259.56 seconds wall clock time: 22 minutes 32.76 seconds (1352.76 seconds total)